fieldelement.py still under testing

Please clear this file soon.

clean up snippets wrt Rdesigneur and/or moogli

testRdesigneur.py
Warning: meshLambda argument is deprecated. Please use 'diffusionLength' instead.
For now rdesigneur will accept this argument.
Error: rdesigneur: Prototype build failed: "elec Proto: global function 'makeCellProto()' not known."
testWigglySpines.py
NeuroMesh::updateShaftParents: may be misaligned
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)
rxdSpineSize.py
Warning: Dsolve::setNinit: Eref z out of range 1, 0
Traceback (most recent call last):
File "rxdSpineSize.py", line 293, in
showVisualization()
File "rxdSpineSize.py", line 191, in showVisualization
makeModel()
File "rxdSpineSize.py", line 120, in makeModel
rdes.buildModel( '/model' )
File "/home/harsha/Jan/moose-core/python/rdesigneur/rdesigneur.py", line 199, in buildModel
self.buildAdaptors()
File "/home/harsha/Jan/moose-core/python/rdesigneur/rdesigneur.py", line 489, in buildAdaptors
self._buildAdaptor( mesh, i[2], i[3], name, i[1], False, i[4], i[5] )
File "/home/harsha/Jan/moose-core/python/rdesigneur/rdesigneur.py", line 1230, in _buildAdaptor
elecComptList = moose.vec( mesh.elecComptList[0].path + '/../spine' )
IndexError: tuple index out of range

Scripts that we did not test on travis

Following scripts were not tested on Travis. These needs to marked OK or dirty
manually. Also see issue #4, and #5

These script launches GUI

These scripts waits for user input

Rdesignuer/ex7.2_CICR examples result not matching as per documentation

With the latest moose-core (git commit "65720c1d2e0eb8")
moose-examples/tutorials/Rdesigneur/ex7.2_CICR.py the result are different as per moose-documentation.
We are looking into this.

Broken scripts are to be ranamed `.py.BROKEN`

If a script a/b/c.py is broken on travis, it will be renamed to a/b/c.py.BROKEN`.

If anyone fix it, please restore it back to its original name.
There are currently 67 scripts which does not pass on travis.

All examples should run with or without moogli installed.

Currently if one can not import moogli, the script raise and exception. import moogli should be optional in all scripts committed to this repository.

moogli and /or morphology

First of all, Moogli doesn't get installed by its own.
The instructions for installation mogli are to be made handy.

While running the insertSpins.py, in absence of the terminal generates
"Warning: Moogli not found. All moogli calls will use dummy functions"

A major issue is with the morphology module.
Running the following files generate error:
"AttributeError: 'module' object has no attribute 'Morphology'"

insertSpines.py
insertSpinesWithoutRdesigneur.py
loadMorphology.py

Running the teseSigNeur.py gives:
AttributeError: 'moose.SynChan' object has no attribute 'synapse'

Scripts that pass on travis or locally

Travis tests each script in this directory. Not all scripts are run. Any script which launches GUI is not executed. Any script which has a call to input() or raw_input() won't run.

Scripts that passed

Scripts that failed

./../paper-2015/Fig2_elecModels/Fig2A.py, Takes too much time, return 137. Not considering a failure now. It runs locally.
./../snippets/nsdf_vec.py

|| Failed with status 1 
  Starting simulation at: 2016-05-06T12:45:05.717483
  Finished simulation at: 2016-05-06T12:45:05.873813
  Closing nsdf handle
  Closed nsdf handle
  Traceback (most recent call last):
    File "nsdf_vec.py", line 178, in <module>
      fname = write_nsdf()
    File "nsdf_vec.py", line 146, in write_nsdf
      pulse_info['delay', ii] = pulsegen.vec[ii].delay[0]
    File "/usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py", line 359, in __setitem__
      raise TypeError("Field name selections are not allowed for write.")
  TypeError: Field name selections are not allowed for write.

Script that did not executed for testing

Rest of them.

Failure when running snippets/loadSbmlmodel.py

Travis reported the following problem:

```

  No CPU information available. Assuming single core.

  No CPU information available. Assuming single core.

  on node 0, numNodes = 1, numCores = 1

  Traceback (most recent call last):

    File "loadSbmlmodel.py", line 106, in <module>

      modelPath, modelpathexist = main()

    File "loadSbmlmodel.py", line 74, in main

      if sbmlId.path != '/':

  AttributeError: 'tuple' object has no attribute 'path'

```

Missing xplot file in demo Fig2A_analysis.py file

python Fig2A_analysis.py 
Traceback (most recent call last):
  File "Fig2A_analysis.py", line 9, in <module>
    fh = open('wt.xplot',mode='r')
IOError: [Errno 2] No such file or directory: 'wt.xplot'

This repository requires cleanup

Currently moose-examples is >30MB is size! It would require to rewriting history after cleanup otherwise we wont be able to reduce the size. Rewriting history means that all forks of moose-examples will become invalid. Many of these files are not required and added inadvertently.

Three largest directories:

13M snippets
6.6M paper-2015
5.2M neuroml

Directories with more than 1MB of content:

2 neuroml/PurkinjeCellPassivePulseInput
2 neuroml/PurkinjeCellPassivePulseInput/cells
2 paper-2015/Fig2_elecModels
2 paper-2015/Fig5_CellMultiscale
2 paper-2015/Fig5_CellMultiscale/cells
2 tutorials/Rdesigneur/cells
3 neuroml/CA1PyramidalCell
3 neuroml/CA1PyramidalCell/cells_channels
3 tutorials
3 tutorials/Rdesigneur
4 paper-2015/Fig6_NetMultiscale
4 paper-2015/Fig6_NetMultiscale/cells_channels
6 neuroml
7 paper-2015

Largest files:

9.6M ./snippets/symcompartment.txt
1.1M ./neuroml/PurkinjeCellPassivePulseInput/cells/purk2.morph.xml
936K ./snippets/threading_demo.dat
736K ./snippets/hdfdemo_Vm.csv
612K ./paper-2015/Fig6_NetMultiscale/cells_channels/CA1spiny7_0.morph.xml
608K ./paper-2015/Fig6_NetMultiscale/cells_channels/CA1spiny.morph.xml
592K ./tutorials/Rdesigneur/chans/CA1.morph.xml
592K ./paper-2015/Fig6_NetMultiscale/cells_channels/CA1.morph.xml
592K ./paper-2015/Fig6_NetMultiscale/cells_channels/CA1.morph.spines.xml
592K ./paper-2015/Fig5_CellMultiscale/chans/CA1.morph.xml
592K ./paper-2015/Fig2_elecModels/chans/CA1.morph.xml
592K ./neuroml/CA1PyramidalCell/cells_channels/CA1_original.morph.xml
592K ./neuroml/CA1PyramidalCell/cells_channels/CA1.morph.xml
592K ./neuroml/CA1PyramidalCell/cells_channels/CA1.morph.original.xml
592K ./neuroml/CA1PyramidalCell/cells_channels/CA1inhomog.morph.xml
588K ./tutorials/Rdesigneur/cells/CA1.morph.xml
588K ./paper-2015/Fig6_NetMultiscale/cells_channels/CA1_nochans.morph.xml
588K ./paper-2015/Fig5_CellMultiscale/cells/CA1.morph.xml
588K ./paper-2015/Fig2_elecModels/cells/CA1.morph.xml
588K ./neuroml/CA1PyramidalCell/cells_ 308K ./genesis/EGFR_MAPK_58.png
252K ./tutorials/Rdesigneur/cells/DHC-neuron.CNG.swc
252K ./paper-2015/Fig5_CellMultiscale/cells/DHC-neuron.CNG.swc
228K ./neuroml/OlfactoryBulbPassive/OBpassive_numgloms3_seed750.0.xml
228K ./.git/objects/pack/pack-9273cc4dcd5076582996dcd1fb1126a024c42053.idx
196K ./snippets/compartmental_neuron.csv
156K ./tutorials/ChemicalBistables/mapkFB.png
152K ./genesis/acc68.png
148K ./neuroml/OlfactoryBulbPassive/cells/mitral.xml
144K ./snippets/output_hdfdemo.h5
136K ./.git/objects/pack/pack-3a08e23cec6c3fdb210083f48ef5b712d9de3287.pack
120K ./paper-2015/Fig4_ReacDiff/CaMKII_merged77.g
116K ./neuroml/OlfactoryBulbPassive/OBpassive_slice_numgloms2_seed100.0.xml
112K ./tutorials/Rdesigneur/cells/VHC-neuron.CNG.swc
112K ./paper-2015/Fig5_CellMultiscale/cells/VHC-neuron.CNG.swc
112K ./paper-2015/Fig2_elecModels/cells/VHC-neuron.CNG.swc
108K ./tutorials/ChemicalOscillators/turingPatternTut.png
96K ./tutorials/Rdesigneur/cells/970529c.CNG.swc
96K ./paper-2015/Fig5_CellMultiscale/cells/970529c.CNG.swc
88K ./.git/objects/53/b4aa1a161381171b0779b3686282666076eedd
84K ./hopfield/hopfield_ui.py
80K ./hopfield/hopfield_ui.ui
76K ./snippets/lifcomp.csv
76K ./genesis/acc35.g
72K ./tutorials/Rdesigneur/cells/barrionuevo_cell1zr.CNG.swc
72K ./snippets/barrionuevo_cell1zr.CNG.swc
68K ./.git/index
52K ./tutorials/ChemicalOscillators/relaxOsc_tut.png
48K ./genesis/Osc_cspace_ref_model.png
48K ./genesis/Kholodenko.png
44K ./squid/squid_demo_qt5.py
44K ./squid/squid_demo.py
44K ./snippets/nsdf_demo.h5

Remove scripts based on `moose.Func` | deprecated

Func was the initial version of the feature and Function was an improved version. The field signatures are slightly different - Func can take 2 or 3 variable messages (xy, xyz). I would suggest checking the existing scripts and use cases to see if Func has any practical utility. Otherwise just deprecate it.

Originally posted by @subhacom in BhallaLab/moose-core#366 (comment)

Genesis load error

Loading genesis file 'genesis/reaction.g' is failing with this release. Following is the traceback.
The script is snippets/savemodel.py.

ReadKkit::setMethod: option  not known, using Exponential Euler (ee)
Traceback (most recent call last):
  File "snippets/savemodel.py", line 67, in <module>
    written = write('/model', 'testsave.g')
  File "/usr/lib/python2.7/site-packages/moose/genesis/_main.py", line 66, in write
    cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
  File "/usr/lib/python2.7/site-packages/moose/genesis/_main.py", line 278, in autoCoordinates
    position = nx.graphviz_layout(G, prog = 'dot')
  File "/usr/lib/python2.7/site-packages/networkx/drawing/nx_pydot.py", line 257, in graphviz_layout
    return pydot_layout(G=G,prog=prog,root=root,**kwds)
  File "/usr/lib/python2.7/site-packages/networkx/drawing/nx_pydot.py", line 277, in pydot_layout
    D=P.create_dot(prog=prog)
  File "/usr/lib/python2.7/site-packages/pydot.py", line 1802, in <lambda>
    lambda f=frmt, prog=self.prog : self.create(format=f, prog=prog))
  File "/usr/lib/python2.7/site-packages/pydot.py", line 2023, in create
    status, stderr_output) )
pydot.InvocationException: Program terminated with status: 1. stderr follows: Error: /tmp/tmpL19Zsb: syntax error in line 2 near ','

Some files in neuroml are not running

@adityagilra

Aditya,
These are not running, bcos of recent update in moose, in which if moose object exist and if we try to create same object (path) with different type/class, it complaints. "To get the existing object use moose.element(obj) instead"
Earlier moose was silently assigning the old id to new variable which was wrong which is corrected.
E.g
pool = moose.Pool('/model/Ca')
reac = moose.Reac('/model/Ca')
reac had moose id of pool which was wrong

twoLIFxml_firing

postcomp = moose.Compartment(post_path)
TypeError: cannot convert LIF to moose.Compartment. To get the existing object use moose.element(obj) instead

somaIKCa = setupTable('somaIKCa',moose.HHChannel(soma_path+'/Gran_KCa_98'),'Gk')
TypeError: cannot convert HHChannel2D to moose.HHChannel. To get the existing object use moose.element(obj) instead

some files while ploting gets seg fault

crossComptNeuroMesh.py ,
crossComptSimpleReac.py,
crossComptSimpleReacGSSA.py,
reacDiffConcGradient.py

These program which are in snippets folder, when run first time it runs fine, but multiple time run gives seg fault like (heisenbug )

Failed scripts on Travis

Following scripts failed/did not run on travis. Connected to issue #4

Using Deprecated API

Blacklisted

./../paper-2015/Fig2_elecModels/Fig2A.py, This takes too much time to run
on travis.

Following scripts are breaking with this release

Many of them due to moogli which is now built with openscene-3.2.1 . The problem should be due to new version of openscene library.

paper-2015/Fig2C.py

File "Fig2C.py", line 356, in <module>
    main()
  File "Fig2C.py", line 337, in main
    rdes = buildRdesigneur()
  File "Fig2C.py", line 148, in buildRdesigneur
    rd.addSpineProto() # This adds a version with an LCa channel by default.
  File "/usr/lib/python2.7/dist-packages/rdesigneur/rdesigneurProtos.py", line 348, in addSpineProto
    assert( moose.exists( parent ) ), "%s must exist" % parent
AssertionError: /library must exist

paper-2015/Fig2D.py

ReadSwc: cells/ko20x-07.CNG.swc : NumSegs = 152, bad = 0, Validated = 1, numBranches = 40
ReadSwc::diagnostics: undef :   0
ReadSwc::diagnostics: soma :    3
ReadSwc::diagnostics: axon :    0
ReadSwc::diagnostics: dend :    59
ReadSwc::diagnostics: apical :  53
ReadSwc::diagnostics: dend_f :  7
ReadSwc::diagnostics: dend_e :  11
ReadSwc::diagnostics: custom :  0
ReadSwc::diagnostics: bad :     0
ReadSwc::diagnostics: undef :   0
ReadSwc::diagnostics: axon_f :  0
ReadSwc::diagnostics: axon_e :  0
ReadSwc::diagnostics: apical_f :        9
ReadSwc::diagnostics: apical_e :        10
Rdesigneur: Elec model has 152 compartments and 0 spines on 0 compartments.
Setting Up 3D Display
QGLTempContext: No GL capable X visuals available.
QGLTempContext: No GL capable X visuals available.
QGLContext::makeCurrent(): Cannot make invalid context current.
Error: OpenGL version test failed, requires valid graphics context.
Segmentation fault

paper-2015/Fig2E.py

Rdesigneur: Elec model has 152 compartments and 0 spines on 0 compartments.
Setting Up 3D Display
QGLTempContext: No GL capable X visuals available.
QGLTempContext: No GL capable X visuals available.
QGLContext::makeCurrent(): Cannot make invalid context current.
Error: OpenGL version test failed, requires valid graphics context.
Segmentation fault

paper-2015/Fig4_ReacDiff/rxdSpineSize.py

Traceback (most recent call last):
  File "rxdSpineSize.py", line 293, in <module>
    showVisualization()
  File "rxdSpineSize.py", line 191, in showVisualization
    makeModel()
  File "rxdSpineSize.py", line 120, in makeModel
    rdes.buildModel( '/model' )
  File "/usr/lib/python2.7/dist-packages/rdesigneur/rdesigneur.py", line 199, in buildModel
    self.buildAdaptors()
  File "/usr/lib/python2.7/dist-packages/rdesigneur/rdesigneur.py", line 489, in buildAdaptors
    self._buildAdaptor( mesh, i[2], i[3], name, i[1], False, i[4], i[5] )
  File "/usr/lib/python2.7/dist-packages/rdesigneur/rdesigneur.py", line 1230, in _buildAdaptor
    elecComptList = moose.vec( mesh.elecComptList[0].path + '/../spine' )
IndexError: tuple index out of range

Script `hopfield/hopfield.py` needs fixing

File "hopfield.py", line 191, in <module>
    test()
  File "hopfield.py", line 145, in test
    hopF = HopfieldNetwork(100)
  File "hopfield.py", line 24, in __init__
    self.createNetwork()
  File "hopfield.py", line 83, in createNetwork
    cell.synapse.num = self.numNeurons
AttributeError: 'moose.IntFire' object has no attribute 'synapse'

Rdesignuer/ex8.3_spine_vol_change.py getting runtime error

commit 17e1dd19046 the file runs but result as show in the doc to the result what is displayed is slightly different

2.After git commit c385807 the example stop working
File "/home/harsha/MOOSE/delete-moose-core/python/rdesigneur/rdesigneur.py", line 1393, in _configureSolvers
dmdsolve.buildNeuroMeshJunctions( smdsolve, pmdsolve )
RuntimeError: getFieldPropertyDestFinfo2::NotImplemented buildNeuroMeshJunctions for rttType Id,Id for oid /model[0]/chem[0]/dend[0]/dsolve[0]

3.After git commit eafa8b2bfe0
RuntimeError: getLookupValueFinfoItem::NotImplemented error

Snippets/Izhikevich_with_synapse.py

Traceback (most recent call last):
File "Izhikevich_with_synapse.py", line 133, in
model_dict = make_model()
File "Izhikevich_with_synapse.py", line 110, in make_model
synapse, spike_in = make_synapse('/model/synapse')
File "Izhikevich_with_synapse.py", line 88, in make_synapse
syn.synapse.num = 1
AttributeError: 'moose.SynChan' object has no attribute 'synapse'

Most tests in `traub_2005` directory are failing with same error

Most scripts in traub_2005 directory are failing, they are emit the following message:

 File "test_nachans.py", line 38, in <module>
    import testutils
  File "/home1/dilawars/SVN/GITHUB/BhallaLab/moose-examples/traub_2005/py/testutils.py", line 45, in <module>
    import channelbase
  File "/home1/dilawars/SVN/GITHUB/BhallaLab/moose-examples/traub_2005/py/channelbase.py", line 165, in <module>
    class ChannelBase(moose.HHChannel, ChannelMeta):
TypeError: Error when calling the metaclass bases
    multiple bases have instance lay-out conflict

Run with moose version 3.2.1-dev20200325

Status of this repositry on Feb 25, 2020. After PR merge BhallaLab/moose-core#387

Following are failing. This is related to BhallaLab/moose-core#388 . The order in unzombification could be determined.

moose-examples/snippets/switchKineticSolvers.py

moose-examples/snippets/savemodel.py

loading model from genesis into moose, and converting it again to genesis one.

File "savemodel.py", line 60, in
written = write('/model', 'testsave.g')
NameError: name 'write' is not defined

Animation in Documentation?

I was thinking of putting animation plots as videos in documentation. It is possible through the Sphinx.

If you permit it, I would like to have animation videos of following python files in snippets folder.
for time plots

loadMorphology.py

For animation plot

reacDiffBranchingNeuron.py
crossComptNeuroMesh.py

Following is a like to the guide how it can be done using pylot.
https://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/

Data files should be in one folder to avoid multiple copies

Currently each example has its own data file in its own folder. This causes lot of problem when packaging due to duplicate file warnings.

Ideally all data files should be kept in one place and let the examples read them from here.

Running but not appropriately presented

Following files run properly without any issues, but do not provide any graphs or output text on terminal.

(I think as they are snippets, an user should get something to understand what just happened while execution of the files.)

multiComptSigNeur.py
Intfire.py

The following file runs properly, and generates graphs, too. It might be easier for a new user to understand if graphs would be labeled.

reacDiffSpinyNeuron.py

Following file runs properly and generates output properly.
But in one of the comments it says the graph runs for 100 milliseceonds, while the command is moose.start(50), so am changing that data in comment.

funcInputToPools : moose.start( 50.0 )

files in snippets needs clean up

Following scripts do not run due to deprecated API

Izhikevich_with_synapse.py Commenting these line 88 to 92 and103, runs the model
testSigNeur.py
wildcard.py

runs but gives

Elements Matching:', '/alfa/##[FIELD(Gbar)=1e-6]')
Error: SetGet::strGet: Field Gbar not found on Element gateX

ex8.1_synTrigCICR result don't match as per documentation

With the latest moose-core (git commit "65720c1d2e0eb8")
moose-examples/tutorials/Rdesigneur/8.1_synTrigCICR and ex8.2_multiscale_gluR_phosph_3compt.py the result are different as per moose-documentation.
Git commit 50f03b getting same result as it is in moose docs need to see what changed over the time

moose-examples/snippets/savempdel.py

Traceback (most recent call last):
File "savemodel.py", line 60, in
written = moose.write('/model', 'testsave.g')

Qt4 to Qt5

Following scripts uses pyqt4 and are not tested, they need to ported to PyQt5.

PYQT_REQUIRED

bhallalab / moose-examples Goto Github PK

moose-examples's People

Contributors

Stargazers

Watchers

Forkers

moose-examples's Issues